old_helpers.py

import re
import os
import MySQLdb
from flask import jsonify

def generate_LPAT_config(start, start_name, target, target_name, carbon_track, allow_reversible, search_id):

    config = "DBHOST\tlocalhost\n"
    config += "DBPORT\t3306\n"
    config += "DBNAME\tMetaDB_2015\n"
    config += "DBUSER\tMetaDBUser\n"
    config += "DBPASS\tmeta\n"
    config += "MOLDIR\tsearches/rpair_mol\n"
    config += "RPAIRDIR\tsearches/rpair_only_maps\n"
    config += "REACTIONDIR\tsearches/rpair_maps\n"
    config += "K\t1000000\n"
    config += "USEREVERSE\t1\n"
    config += "STARTCID\t" + start + "\n"
    config += "TARGETCID\t" + target + "\n"
    config += "CARBONTRACK\t" + carbon_track + "\n"
    config += "PERCENTCARBON\t1.0\n"
    config += "WEIGHTTYPE\tWEIGHT_OF_ONE\n"

    output_loc = "searches/output/" + search_id + "|" + start_name + " (" + start + ")|" + target_name + " (" + target + ")|" + "LPAT.txt"
    output_loc = output_loc.replace(" ", "_")
    config += "OUTPUTDIR\t"+ output_loc + "\n"

    input_loc = write_config_file(search_id, config)
    print config
    return input_loc, output_loc

def generate_hub_config(start, start_name, target, target_name, carbon_track, allow_reversible,
        search_id, hub_list, hub_db):

    config = "DBHOST\tlocalhost\n"
    config += "DBPORT\t3306\n"
    config += "DBNAME\tMetaDB_2015\n"
    config += "DBUSER\tMetaDBUser\n"
    config += "DBPASS\tmeta\n"
    config += "MOLDIR\tsearches/rpair_mol\n"
    config += "RPAIRDIR\tsearches/rpair_only_maps\n"
    config += "REACTIONDIR\tsearches/rpair_maps\n"
    config += "K\t1000000\n"
    config += "USEREVERSE\t1\n"
    config += "STARTCID\t" + start + "\n"
    config += "TARGETCID\t" + target + "\n"
    config += "CARBONTRACK\t" + carbon_track + "\n"
    config += "PERCENTCARBON\t1.0\n"
    config += "WEIGHTTYPE\tWEIGHT_OF_ONE\n"
    config += "HUBTABLE\tsearches/" + hub_db + "\n"
    config += "IGNORE_CMPD\tsearches/" + hub_list + "\n"
    config += "NUMCLOSESTHUBS\t3\n"
    config += "HUBSEARCHDEPTH\t10\n"
    config += "MAXRXNINHUBPATH\t10\n"

    output_loc = "searches/output/" + search_id + "|" + start_name + " (" + start + ")|" + target_name + " (" + target + ")|Hub|" + hub_db + ".txt"
    output_loc = output_loc.replace(" ", "_")
    config += "OUTPUTDIR\t"+ output_loc + "\n"

    input_loc = write_config_file(search_id, config)
    return input_loc, output_loc


#
# Helpers
#

def write_config_file(search_id, config):
    config_loc = "searches/input/" + search_id + ".txt"

    config_file = open(config_loc, 'w')
    config_file.write(config)
    config_file.close()

    return config_loc

def get_canonical_cmpds(goal):
    filename = "searches/canonical_pathways/" + goal + ".txt"
    if os.path.isfile(filename):
        canonical_cmpds_file = open(filename, "r")
        canonical_paths = canonical_cmpds_file.readlines()
        canonical_cmpds = []
        if canonical_paths != None:
            for canonical_path in canonical_paths:
                cmpd_pairs = re.findall("C[0-9]{5}-C[0-9]{5}",canonical_path)
                canonical_cmpds.append(cmpd_pairs)
            return canonical_cmpds
    return ""


def get_min_len_and_num_hub_paths(hub_cursor, hub1, hub2):
    hub_cursor.execute("SELECT paths FROM " + hub1 + "_" + hub2 + "")
    paths = hub_cursor.fetchall()
    num_paths = 0
    min_length = 100
    for item in paths:
        raw_paths = item[0].split("},")
        num_paths += len(raw_paths)

        split_path = raw_paths[0].split("\t")
        if len(split_path) < 3:
            continue
        current_length = int(split_path[1].replace(".0",""))
        if current_length < min_length:
            min_length = current_length

    return str(num_paths) + "," + str(min_length)




def extract_pathways(string_pathways, background_hubs_filename, hub_db):
    pathways = []
    all_hub_nodes = set([])
    all_hub_links = []
    # Finds compound IDs by extracting words that start with the letter 'C'
    regex = re.compile("C\w+")
    regex2 = re.compile("RP[0-9]{5}")

    start = None
    goal = None
    hubs_exist = False
    rxn_db = {}
    db = MySQLdb.connect(host="localhost", user="MetaDBUser", passwd="meta", db="MetaDB_2015")
    cursor = db.cursor()

    hub_db_object = MySQLdb.connect(host="localhost", user="MetaDBUser", passwd="meta", db=hub_db)
    hub_cursor = hub_db_object.cursor()

    canonical_links = list()
    canonical_cmpds = list()

    for string_path in string_pathways:
        if string_path == "":
            continue
        atp_used = 0
        hub_len = 0
        tab_split_path = string_path.split("\t")
        carbons_conserved = []
        if len(tab_split_path) > 1:
            carbons_conserved = re.findall("[0-9]+=[0-9]+", tab_split_path[-1])
        if len(tab_split_path) == 3:
            atp_used = int(tab_split_path[-2].replace(".0",""))
        if len(tab_split_path) == 4:
            hub_len = tab_split_path[1]
        path_compounds = regex.findall(string_path)
        path_rpairs = regex2.findall(string_path)
        path_rxns = []

        if len(path_compounds) == 0:
            continue

        for rpair in path_rpairs:
            if rpair not in rxn_db:
                cursor.execute("SELECT KEGGReactionID FROM KEGGReactionsRpair WHERE KEGGRpairID='" + rpair + "'")
                list_of_rxns = []
                for item in cursor.fetchall():
                    list_of_rxns.append(item[0])
                rxn_db[rpair] = list_of_rxns

            path_rxns.append(rxn_db[rpair])

        print path_compounds
        print path_rpairs
        nodes = set([])
        links = []
        hub_nodes = set([])
        hub_links = []

        if start == None and goal == None:
            start = path_compounds[0]
            goal = path_compounds[-1]

        rpair_idx = 0

        for i in range(len(path_compounds) - 1):
            j = i + 1
            if ("_HS" in path_compounds[i] and "_HE" in path_compounds[j]) or ("_HS" in path_compounds[i] and "_HM" in path_compounds[j])  or ("_HM" in path_compounds[i] and "_HM" in path_compounds[j]) or ("_HM" in path_compounds[i] and "_HE" in path_compounds[j]):
                hubs_exist = True
                hub_nodes.add(path_compounds[i])
                hub_nodes.add(path_compounds[j])
                min_len_num_hubs = get_min_len_and_num_hub_paths(hub_cursor, path_compounds[i][0:6], path_compounds[j][0:6])
                hub_links.append(path_compounds[i][0:6] + "-" + path_compounds[j][0:6] + ":" + min_len_num_hubs)
            else:
                #print "length of path compounds"
                #print path_compounds
                #print "length of path rxns"
                #print len(path_rxns)
                links.append(path_compounds[i][0:6] + "-" + path_compounds[j][0:6] + ":" + ",".join(path_rxns[rpair_idx]))
                rpair_idx += 1

        pathway = {}
        pathway["atoms"] = carbons_conserved # TODO: actually calculate this
        pathway["atp"] = atp_used
        pathway["nodes"] = [node[0:6] for node in (set(path_compounds) - hub_nodes)]
        pathway["links"] = list(links)
        pathway["hub_nodes"] = [hub_node[0:6] for hub_node in hub_nodes]
        pathway["hub_links"] = list(hub_links)
        pathway["hub_len"] = int(hub_len)
        #pathway["canonical"] = is_pathway_canonical(path_compounds, start, goal)
        pathways.append(pathway)
        if(hubs_exist):
            all_hub_links = all_hub_links + hub_links

        canonical_paths = get_canonical_cmpds(goal)
        canonical_links = set([])
        canonical_cmpds = set([])
        if canonical_paths != None:
            for canonical_cmpd_pairs in canonical_paths:
                canonical_links = set(canonical_cmpd_pairs) | canonical_links
                for canonical_cmpd_pair in canonical_cmpd_pairs:
                    cmpds = canonical_cmpd_pair.split("-")
                    canonical_cmpds.add(cmpds[0])
                    canonical_cmpds.add(cmpds[1])

        canonical_links = list(canonical_links)
        canonical_cmpds = list(canonical_cmpds)

    cursor.close()
    pathways_data = {
        "info" : {
            "start" : start,
            "goal" : goal,
            "canonical_nodes" : canonical_cmpds,
            "canonical_links" : canonical_links,
            },
        "hub_db" : hub_db,
        "pathways" : pathways,
    }

    # If this is a hub search, add in the rest of the hubs
    if(hubs_exist):
        #pathways_data["background_hubs"] = get_background_hubs_from_file(background_hubs_filename, set(all_hub_links))
        pathways_data["background_hubs"] = get_background_hubs_from_file(background_hubs_filename)

    return pathways_data

# def get_background_hubs_from_file(background_hubs_filename, all_hub_links):
#     b_hubs_file = open(background_hubs_filename, "r")
#     b_nodes = {}
#     b_links = []
#     on_links = False
#     for line in b_hubs_file:
#         line.replace("\n", "")
#         if not on_links:
#             if "LINKS" not in line:
#                 node_info = line.split(",")
#                 b_nodes[node_info[0]] = (float(node_info[1]), float(node_info[2]))
#             else:
#                 on_links = True
#         else:
#             if(line not in all_hub_links):
#                 b_links.append(line.replace("\r","").replace("\n",""))

#     return { "b_nodes" : b_nodes, "b_links" : b_links }

def get_background_hubs_from_file(background_hubs_filename):
    b_hubs_file = open(background_hubs_filename, "r")
    return b_hubs_file.read().split("\n")


def get_pathways_from_file(pathways_filename, background_hubs_filename, hub_db):
    pathways_file = open(pathways_filename, "r")
    return extract_pathways(pathways_file.readlines(), background_hubs_filename, hub_db)


def hub_paths_to_json(hub_src, hub_dst, hub_db, string_hub_pathways):
    pathways = []
    rxn_db = {}
    db = MySQLdb.connect(host="localhost", user="MetaDBUser", passwd="meta", db="MetaDB_2015")
    cursor = db.cursor()

    # Finds compound IDs by extracting words that start with the letter 'C'
    regex = re.compile("C\w+")
    regex2 = re.compile("RP[0-9]{5}")

    for string_path in string_hub_pathways:
        paths = string_path[0].split("},")
        for path in paths:
            raw_atoms = re.findall("[0-9]+",path.split("{")[1])
            path_atoms = len(raw_atoms)
            print raw_atoms
            path_compounds = regex.findall(path)
            path_rpairs = regex2.findall(path)
            
            if len(path_compounds) <= 1:
                continue

            path_rxns = []
            for rpair in path_rpairs:
                if rpair not in rxn_db:
                    cursor.execute("SELECT KEGGReactionID FROM KEGGReactionsRpair WHERE KEGGRpairID='" + rpair + "'")
                    list_of_rxns = []
                    for item in cursor.fetchall():
                        list_of_rxns.append(item[0])
                    rxn_db[rpair] = list_of_rxns

                path_rxns.append(rxn_db[rpair])

            links = []
            for i in range(len(path_compounds) - 1):
                j = i + 1
                links.append(path_compounds[i] + "-" + path_compounds[j] + ":" + ",".join(path_rxns[i]))

            pathway = {}
            pathway["atoms"] = path_atoms # TODO: actually calculate this
            pathway["nodes"] = path_compounds
            pathway["links"] = links

            # Empty list since hub pathways don't contain hubs themselves
            pathway["hub_links"] = []
            pathway["hub_nodes"] = []

            pathways.append(pathway)


    hub = {
        "info" : {"source" : hub_src, "target" : hub_dst},
	   "hub_db" : hub_db,
        "pathways" : pathways
    }
    return jsonify(hub)


def remove_input_file(search_id):
    os.remove("searches/input/" + search_id + ".txt")